I run a pen and paper rpg, started out as 2nd Edtion Dnd, where I asked for help creating Knight Houses a while back, but switched over to Pathfinder, since it gave more variance in character creation for the players. I need some suggestion and input for Gods and Deities in my campaign, but any other ideas, be it kingdoms, characters, villians, npc's, are also welcome.

Oh boy. [Cracks knuckles]
Most of ny inspiration comes from Fire Emblem and The Witcher. So I suggest looking to them, or Skyrim for great ideas.
Have a saint that one of your clerics follow. The patron saint of luck, maybe. One that carries a staff and gives a +2 bonus to Wisdom anytime someone rolls a nat 13. Maybe this saint can be exposed as a dark witch or something, and then after a nat 13 suffers a penalty of -2. It's your call.
Have a mysterious peddler that shows up right before boss battles (Like Chocolina from FFXIII-2). Make your players associate big battles with that peddler. Then the peddler joins your party or becomes the final boss.
Have a place that can only be discovered with a nat 20 on perception. A medically advanced place, or maybe it's a weapons cache. Have a weapon you can buy that turns enemies to golden dust. Make a chicken talk and be the key to victory. Have a npc named Pitty that has bad suggestions and misleads characters.